Showing : Rnaseq • reset
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how to create PHENO_DATA
RNASeq RNASeqData RNASeqRData
3.1 years ago marymshahi2021 • 0
0
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2
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2.4k
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maSigPro: how to extract the genes in the same cluster
rnaseq
updated 3.1 years ago by • 0 • written 9.5 years ago by ▴ 10
1
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2
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769
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how to plot the union of the 100 most expressed genes
DESeq2 RNASEQ
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by • 0
0
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1
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1.4k
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Correlation between two different datasets: between results of RNAseq and absence/presence of Type3 Secretion System
RNASeq Correlation DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
2
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8
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3.0k
views
Error in Create switchAnalyzeRlist
AlternativeSplicing RNASeq IsoformSwitchAnalyzeR gtf
written 3.2 years ago by ▴ 10
0
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2
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2.6k
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks RNASeq CancerData
updated 3.2 years ago by ▴ 270 • written 3.3 years ago by • 0
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0
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791
views
DEXSeq aggregated genes/exons result in NA values
RNASeq R DEXSeq
3.2 years ago osieman52 • 0
4
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5
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3.4k
views
Which is the best type of data for correlation or survival analysis
TPM RNASeq RSEM DESeq2
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 10
1
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1
reply
802
views
Handling heterogeneous data in DESeq2: multiple covariates to control against
RNASeq DESeq2
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
1
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5
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3.1k
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DESeq2 outlier options and LFC Shrinkage
DESeq2 RNASeq RnaSeqSampleSize apeglm
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
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6
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2.2k
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Is DESeq2 generating false postives when changing different pre-filtering thresholds?
RNASeq DEG DESeq2
3.2 years ago Weiqian ▴ 10
0
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0
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594
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Can I loosely say that a gene is expressed by simply look at the gene count from RNA-Seq?
RNASeqData RNASeq
3.2 years ago Pang • 0
1
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1
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1.3k
views
Filtering Orthologus Genes Before or After TMM normalization?
RNASeq Normalization TMM edgeR
updated 3.2 years ago by 53k • written 3.2 years ago by ▴ 10
0
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2
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1.4k
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IsoformSwitchAnalyzeR package on mouse data
rnaseq IsoformSwitchAnalyzeR
updated 3.2 years ago by ▴ 120 • written 3.2 years ago by • 0
0
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1
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1.4k
views
Job: 'Omics data analyst for HPCBio, University of Illinois
Metagenomics GenomicVariation Genomics RNASeq ChIPSeq
3.2 years ago Jenny Drnevich ★ 2.0k
5
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6
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2.6k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM avereps voom limma RNASeq
3.2 years ago Yang Shi ▴ 10
1
vote
5
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1.3k
views
DeSeq2 Matched Analysis
RNASeq DESeq2
3.2 years ago Andrea • 0
3
votes
4
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1.5k
views
Can I use limma::avereps to remove dupicated genes before conduct DEG based on RSEM Expected_count data?
limma RNASeq Expected_count DESeq2
3.2 years ago Yang Shi ▴ 10
1
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2
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3.0k
views
DEseq2 anlysis - LfcThreshold and Lfcshrink options
lfcshrink DESeq2 RNASeq lfcthreshold
3.3 years ago • updated 3.2 years ago ClaudiaE • 0
1
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0
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890
views
Which algorithm would you use for the cell-cell communication analysis of bulk RNA seq datasets?
RNASeq
3.3 years ago curiousmind007 ▴ 10
3
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4
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3.5k
views
Why Negative value from GSVA
GSVA RNASeq edgeR
3.3 years ago Yang Shi ▴ 10
5
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8
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27k
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Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 14 months ago by ▴ 60 • written 3.3 years ago by ▴ 30
2
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2
replies
1.3k
views
Can't load UCSC transcript IDs
RNASeq
updated 3.3 years ago by ★ 4.1k • written 3.3 years ago by • 0
2
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4
replies
2.3k
views
deseq2 lfc shrinkage with few DEGs
RNASeq DESeq2
updated 6 months ago by 43k • written 3.3 years ago by ▴ 10
3
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3
replies
1.3k
views
Nested analysis or Collapsed-replicate analysis?
RNASeq DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
votes
1
reply
951
views
lfc Shrinkage with multiple comparison groups
RNAseq lfcShrinkage DESeq2
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
0
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1
reply
756
views
Nested analysis or Collapsed-replicate analysis?
RNASeq DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
1
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1
reply
1.1k
views
RNA-Seq normalization and batch effect removal
RNASeq BatchEffect DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
1
vote
1
reply
1.1k
views
NOIseq Probability column
RNAseq RNASeqData NOISeq
3.4 years ago • updated 3.3 years ago Pratibha ▴ 10
9
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3
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9.5k
views
Limma vs deseq2 results
limma RNASeq R
3.4 years ago k___ ▴ 30
3
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3
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2.4k
views
Question on RNA-Seq single sample data analysis in EdgeR
R edgeR limma RNASeq Normalization
updated 3.4 years ago by 53k • written 3.4 years ago by ▴ 10
3
votes
9
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3.2k
views
Warnings when using "ashr" in lfcshrinkage for DESeq2
RNASeq DESeq2
updated 2.8 years ago by • 0 • written 3.4 years ago by ▴ 20
1
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2
replies
2.2k
views
Looking for a package that compares my RNA seq data to find published dataset with a similar expression pattern
RNASeq
written 3.4 years ago by ▴ 10
1
vote
1
reply
2.1k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 3.4 years ago by 53k • written 3.4 years ago by • 0
1
vote
2
replies
1.7k
views
How to properly use DESeq2 for an experiment
ExperimentalDesign RNASeq DifferentialExpression DESeq2
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
3
votes
11
replies
4.3k
views
RNA-seq: compare two technical replicates
RNASeq
updated 3.4 years ago by 53k • written 3.5 years ago by ▴ 20
0
votes
2
replies
986
views
edgeR
rnaseq edgeR
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
0
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3
replies
6.7k
views
Best way to do RNA-seq analysis for a small number of samples obtained from 2 different batches
RNASeq
updated 3.5 years ago by ★ 1.4k • written 3.5 years ago by • 0
5
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6
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4.2k
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools edgeR pcaExplorer RNASeq RNAseq123
3.5 years ago Alan • 0
0
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0
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1.2k
views
Only 1 gene/ feature is present in module after WGCNA analysis
RNASeq Clustering cluster WGCNA
3.5 years ago chiwut.wong • 0
0
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0
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1.1k
views
Pathway Analysis using GAGE
gage RNASeq gageData Pathways
3.5 years ago OST • 0
6
votes
4
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4.3k
views
confused with tximport counts abundance using salmon input
RNASeq tximport
3.5 years ago Al90 ▴ 10
0
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7
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2.0k
views
DESeq2 on allelic reads
RNASeq DifferentialExpression DESeq2
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
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1
reply
1.0k
views
Rtracklayer
rtracklayer RNASeq gff
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
0
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1
reply
1.2k
views
Differential Expression Analysis-Input is DESeq Standardized
rnaseq RNASeqData limma limmaGUI
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
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3
replies
1.3k
views
DEseq2 Analysis over multiple tissues and conditions only gives 16 coefficients
DESeq2 RNASeq
updated 3.5 years ago by 43k • written 3.5 years ago by • 0
0
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2
replies
2.9k
views
DESeq2 counts distribution across both genes and samples
deseq2 rnaseq
updated 3.5 years ago by • 0 • written 9.1 years ago by ▴ 50
0
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0
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1.0k
views
How to perform transcription factor enrichment analysis (TFEA) for RNA-seq counts data.
TFEA.ChIP RNASeq RNASeqData
3.5 years ago treebig44 ▴ 40
1
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0
replies
854
views
Is that possible to find if the sequence is enriched by specific motifs
MotifDiscovery RNASeq
3.6 years ago Liliian • 0
0
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0
replies
4.2k
views
Create a Gene Enrichment GO plot from goana output
goana RNASeq edgeR RnaSeq GO
3.6 years ago Raito92 ▴ 60
1,409 results • Page 5 of 29
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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